I'm a film hack. Yeah, some of my short vids have hundreds of thousands of views or even millions, and some (nameless) have contributed to big donations, but I'm still a hack. Last fall I had a very very brief moment of insanity when I thought, just thought, fantasized, really, that, maybe, I could do a documentary on iGEM, synthbio, and DIYbio.
Y'see, we're living in the early days of a renaissance in Biology. Wouldn't it be great to capture all that, travel the country, talk science in a broad-sweeping documentary?
But then I realized what it would take for me to do it: being a hack, it would be much harder to get to the level I wanted. The gap between my skill level, equipment access, time, and money and what was needed was way too large, even to try and fund it via Kickstarter.
But then, at iGEM 2010, I bumped into two guys whom I had initially met at iGEM 2009, and who now had a cool project they were working on (see video below).
And I pledged $300. Don't know about you, but $300 is a big deal for me. But, it's also a big deal that this documentary get made.
Will you join me and help these guys get the funds they need?
These guys have great style, sensibility, and focus (loved the trailer, below, and check out the cool excerpts). It's gonna be an awesome documentary and will kick ass at Sundance. But only if you join me in helping them.
What are you waiting for? Head over to Kickstarter and pledge something. Wouldn't you say 25 bucks should help?
Nature has a nice wee article (no subscription required to read this one, FTW!) on the state of what one might call "informal" peer review - the challenges and questions to published works that come from blogs and tweets and the like.
For those of us who have been talking about the changes needed in the whole infrastructure and culture of science discourse (particularly the lock publishers have on research papers), this Nature article holds no surprises. Indeed, it comes off making some scientists seem a bit whiny.
The article points to some recent events where scientists have been skewered online for papers or claims made. This reminds me of the early days of blogging when folks were trying hard to control the message and were freaking out when anyone said anything.
The paper does have some great examples and quotes though. For example, David Goldstein, from Duke's Center for Human Genome Variation, is quoted saying, "if the work is solid, it hold up over time". And the efforts by PLoS with comments on papers, how arXiv.org works, and ratings from F1000 are good to show to those who are probably reading the article to figure out how to survive the blogosphere.
My favorite comment by the author, though, is:
One solution may lie in new ways of capturing, organizing and measuring all these scattered inputs, so that they end up making a coherent contribution to science instead of just fading back into the blogosphere.
I've been harping on this for a while and still think there's an opportunity to create a solution like this. I think there is a lot of good thinking, plenty of examples in other industries, and folks are doing parts of this solution, such as trying to think of other ways to change how we calculate the impact of a paper (à la Technorati or through real-time stats), author ID systems, or ways to turn the science paper into the social object. The article also mentions Jason Priem's work on alternate paper metrics (alt-metrics).
It feels like 2004 all over again as another industry discovers the power of devolving the power back to the masses. And the Web was initially designed by scientists, for scientist - what's there to fear?
UPDATE 28jan11: Related to this topic, Zachary Knight has an incisive commentary on how all this was protrayed.
I mentioned a few weeks back a review in Nature about a trio of scientists studying the contributions of gut microbial ecology in preemies that get necrotizing enterocolitis (NEC). Sneaky, sneaky, it turns out that a paper on this work was posted that the review didn't mention or link to. I subsequently found a great article out of the UC Berkeley media relations team that is an even better review of the work, with some excellent quotes from the investigators themselves.
It's a fascinating story. The microbes in preemie feces were collected daily and either sequenced completely or identified by 16S rRNA sequences. The investigators were then able to visualize a time course of the abundance of different microbes (image to upper-right) and to start to understand the contributions of these microbes to pathology, particularly NEC.
It's cool to see the shifts in population as the gut microbes settle in. Interestingly (and not surprising), there were some microbes that are known to be pathogenic, but didn't really affect the preemie's health.
The thought, though, is that there might be some strain specificity within microbe species, or something related to the balance of all the other bacteria. This seems to correlate well with the findings from folks studying the contribution of gut microbes to immune system development.
If you're into developments in human microbial ecology (which I highly recommend new grad students study), I urge you to read this paper (here's the link from the article linked above) and the back story in the article linked above.
What do you think of this?
Image from the paper showing a time course of the gut microbial species
Our theme is "Making Stuff". Our valley is steeped in a rich history of making stuff, from the straw hat industry of Amherst to Holyoke and Springfield and Northampton. That tradition continues and we'll hear thought-provoking Ignites from folks Making Stuff in our valley.
There'll be folks talking about Fish, Games, Museums, and Biz. I'll be on hand to give a whirlwind tour of DIYBio (working title "The past, present, and future of making stuff through biology").
My plan (working on talk today) will be about all the ways we use biology to make stuff, starting with practical microbiology (of course), then making the leap to synthetic biology, and then spending some time showing examples of all the cool things happening among DIYbio folks. Of course, the emphasis will be on all the "making". And, I'm sure as I develop the outline, I'll start winnowing away the extra and find that one thing I am excited to focus on.
Let's see what actually turns out. The talks will be pecha kucha - 20 slides automatically flipping in 5 minutes - which I've never done before. Thankfully, I do NOT think 5 minutes is too short to share something that excites me.
I have a thing about noise (see my ramblings here). And as folks try to turn elements of biological circuits into well-behaving engineered parts, I’ve been trying to put my finger on why biological noise means so much to me.
The main review mentions that noise is a nuisance in the design of deterministic (engineered) circuits. But goes on to show that noise in biological systems provides critical functions that are hard to achieve with deterministic circuits.
Noise in biological systems is unavoidable, there are limits to how much a feedback system can reduce noise. And the review goes on to discuss many areas where noise is integral to the stability or responsiveness of a process, such as gene expression coordination, state-switching, positive feedback, differentiation, and in development.
How might we understand this noise and actually engineer it into our deterministic circuits?
One thing, though, that tempers my bias towards keeping noise in biologically engineered circuits is that digital electronics also had their start in a noisy analog world. Will engineering biological circuits be forever mired in the analog noisy world of biology or will these circuits eventually be complex enough to exhibit the precise nature that biological engineers seem to want? Should biological engineers seek to incorporate noise into their calculations or strive to limit stochastic fluctuations?
Really, that’s a bit beyond my ability to understand circuit design and noise and all, so I leave it to smarter folk than I. :-)
Here’s a paper from September I haven’t had a chance to comment on.
Zhang et al reported in Science (review, paper - subscription required) how two almost identical protein sequences can have different translational modifications. In this case, β-actin and γ-actin are 98% identical, the differences are marginal and don’t explain why one protein is modified with arginine and the other is not.
The difference is actually quite subtle - there is one amino acid in the protein sequence that is lysine in both proteins, but the codons in the RNA are different. That difference is enough to change the relative translation speed of β-actin so that it rapidly folds and gets arginylated but not degraded as happens in the slower translation of γ-actin. In the end, this affects the relative lifetime of each protein in the cell, leading to differential functions.
That’s so cool.
It seems like every so often, things we view as well understood turn out to have another layer of subtlety built in. For example, differential codon usage is usually considered a synonymous change, nothing momentous. Sure, there’s been studies of codon usage relative to the abundance of corresponding tRNAs and how that might be used to modulate abundance of a protein (a quick Google search revealed some interesting codon-usage papers). But I think this case is novel, differential codon usage actually affecting the post-translational modification of a protein simply by tweaking the speed of translation.
How might we create a codon usage table that takes into account tRNA abundance, contribution to translational speed of different codons, and speed of post-translational processes to be able to model and predict things like the differences between the functions of β-actin and γ-actin.
Also, how prevalent is this subtle effect on post-translational modification and how susceptible is it to breaking and causing trouble in a cell?
image from Science review (found via Google images, mind you)
Lizzie Buchen from Nature (link below) wrote a great article on some cool work folks are doing to change the way we view bacteria.
For example, one group (like a joke, it’s a microbiologist of extremophiles, a neonatologist, and a human microbial geneticist) is studying the effect of bacteria on a devastating intestinal disease in premature babies. They want to know if there’s a role or not for bacteria in this disease.
What’s interesting is that up to now, most understanding of bacteria in humans has been stuff that is pathogenic and can be cultured easily. Bringing in someone who is skilled at finding and characterizing microbes from extremely inhospitable places might help discover new things about our own microbiota.
I don’t know if it’s because I’m all interested now in human microbial ecology or if indeed there has been a resurgence in the study of human microbiology, all I know is that not a week goes by without a new paper or review in this area.
BERG has come out with two more "alternative futures" videos, once again made with Dentsu London and Timo Arnall.
I've been struggling to put into words what I feel and think when I see these visions. I see this as all about ubiquitous computing (ubicomp) or calm computing.
When folks spoke about ubicomp (I remember talking about it back in the 90s) it focused on the computer, the devices, the data, and how it would interface with people. And one theme was that "computing" would recede into the background.
But these videos are much more - much more current with how we use machines and our expectations of how to interact with them and the world. Today, computing and devices are as hum-drum as a newspaper or magazine, no more wondrous than a chair we sit in. All that was ubicomp has finally receded into the mundane.
In Incidental Media (video below) and Media Surfaces: The Journey the focus is on the peripheral (ambient?) "calmness" of information presentation, with a bit of play worked in. Surfaces (printed and digital) become a part of the landscape, much like clouds or smells that provide information should you turn your attention to them.
One key thing that I'd also like to point out is that all this information or activity is modest - it's as smart as a puppy and isn't meant to be a smidgeoun smarter.
What did you think of when you saw these videos?
Video: Incidental Media
And, I got to say I chuckled a few times when I saw some of the names in the videos and that Finnish coaster. Nice touches for those who know. :-)
Services like Twitter and Facebook have centralized our communications, such that we depend on their skills to keep their part of the network up (let alone, safeguarding all the data they collect from us). But, unlike electricity companies and telcos, who have their pseudo-monopolies highly regulated, we are stuck _trusting_ that Twitter and Facebook won't do us harm.
But how many times will we allow them to shut down their service or play games with our data?
Twitter this week seems unable to stay up. Or, maybe they are just spreading out failure rather than having a total melt-down (a micro-down?).
I think this would not be happening if all our communications and data lived in our hands rather than someone's servers in the Cloud.
It was a night of culture - yoghurt cultures. Vaughn Tan shared his passion for yoghurt with about two dozen captivated future yoghurt makers. He spoke about the biochemistry and microbial ecology of the process - ways to optimize the proteins in the milk, effects of inoculation temperatures, the activities of the different bacterial populations in the culture.
Complex systems The coolest thing Vaughn explained was about the three key populations of bacteria in yoghurt, their optimum growth temperatures, and how he varied inoculation temperatures to encourage the right populations of bacteria to grow. He pointed out that the usual yoghurt recipes keep the yoghurt culture at a single temperature; this likely diminishes the cultural diversity, reducing the quality of the yoghurt. It was clear that Vaughn’s delicious yoghurt benefitted from a multi-organismal systems understanding.
Ancient cultures Of course, he brought samples (tasty!) and encouraged everyone to take a bit home. The story around this strain was that Vaughn got it from the Google yoghurt three years ago, and the Google cook apparently got the strain from India, where it was already 500 years old, so we joked that the strain was 503 years old.
But Vaughn mentioned that these complex cultures are always changing, so they really are not the same culture when folks take samples to new places. Also, most cultures come from a previous one unless someone starts one from nature, so it’s highly likely this culture might be even older than we think.
Vaughn was also encouraging us to take some home as an insurance that this strain never dies out. That made me feel that I’ve become part of Vaughn’s network of apprentices, carrying the “flame” of this strain.
The cultured crowd Vaughn led a great discussion, and the audience was quite engaged. Mac posed a great question regarding the copyright of strains, if there were legal ramifications to using strains taken from commercial yoghurts, such as from Vaughn’s favorites Stonyfield and Seven Sins (I think that's what it was called). I joked that commercial strains could be fingerprinted for copyright protection.
In the spirit of Folk Microbiology, Keegan brought his microbial battery. It also uses a heterogeneous bacterial culture of aerobic and anaerobic bacteria to create a useful electric gradient.
Also, I brought a few bottles of my own home-brew (an IPA) for everyone to enjoy. Alas, my brew was started with commercial yeast, most likely mono-cultural, though, no doubt, itself an old strain. Vaughn urged me to experiment with lambic-style open-air inoculation of my beer, with the potential benefits of a heterogeneous culture. Heh. Could be interesting. And since sometimes I inoculate with a bottle from the previous batch, I could then start my own strain of beer yeast to hand down to future generations of home brewers.
Awesome experience As an aside: I brought my 15 year old son along. My highlight of the evening was watching his wonder as he met with everyone, saw their demos, read some books off the shelves, and, basically, saw that there are many ways to express one’s curiosity and creativity. From dirt batteries, to electronic poi, to ancient bacterial cultures, his expanding world was pure joy for me.
"Take back the graph!" was @mattmiz's reply to my rant that The Cloud was shite, Facebook was poison, and that the future will be peer-to-peer social networking.*
Head in the clouds How did I come about to that, since not long ago, I was Mr Cloud, harping about a time when all would be in the Cloud, with a dashboard (or a "door") to all our lifestreams, connecting to everyone, sharing, loving, communicating?
At least, that was the original vision of Ovi I first pitched at the end of 2005 (to the wrong crowd, though). I thought that the killer service would be Cloud-based and full of lifestreams. The last flourishes on these thoughts in the past years revolved around visualization and filtering of all these streams.
But I believe this no more.
Here is where I rain on everyone's parade Facebook is the best example of how Cloud living can go wrong. Folks who are first discovering social networking are getting so mired in Facebook without understanding how Facebook is so twisted with respect to the users.**
And nothing is really in the Cloud. Is anything ever really in the Cloud? No, everything has always been on someone's servers. Their servers. Your data, their servers. [Despite this, there have been efforts to take back the graph, great standards work to democratize social networking - see here a suggested alternative.]
So, I say, The Cloud is a fantasy.
The past is future Back in my father's day, data resided on someone else's machine. When I started with computers, it was the dawn of PCs, where the data resided on my machine. Then we hooked up all those PCs to communicate until some of those PCs got huge and ended up shouldering the work, serving up data stored out there somewhere.
And now The Cloud dream is to return to a time where the "terminal" is an appendix on the network, and that the network would store everything and do all the work. Terminals are to be just windows onto the Cloud, Just as our terminals were getting interesting and wide-spread - smartphones, tablets, amazing laptops.
How did we let that happen again? Bad move.
Peer to peer social networking I claim that we need to move data and communication back to the edge of the network, residing in your machines, sitting in your hands, your laps, your tables.
I used to say that the ultimate social networking device was the mobile phone - your buddy list in your address book, billions and billions of text messages exchanged, a direct 1-1 link through a phone call.
Can that model be extended? Can we create a world where there is no Cloud, just a bunch of network bots pushing packets, be they IP or SMS or whatever communication packet we need to route? What will a peer-to-peer email-blogging-website-social network be like?
Do you want to have full control over your data, your social graph, your communications, just like you do now with your mobile phone?
So do I.
How will we do it?
*I've not really written these thoughts down before, since I've sort of stopped
worrying (or at least tried to), or hoped to do something myself. They
are peppered in the bookmarks and comments I have made in the past
years, though. And since I have a high idea to execution ratio, here's the thought for anyone to build upon.
**I deleted my first Facebook account in 2008. I only got another one last year because of work. But, yeah, it'll be gone as soon as I can ditch it.
One thing I've noticed here in the US is that there is trash everywhere, collecting in the "unspace", places where there is no movement or wind or people to brush them away.
A few things stick out - styrofoam cups, plastic drink covers, and plastic bags.
My proposal: Plastic is to be prohibited for uses where the lifetime of use is less than a day.
Can we start with that?
Starbucks and Dunkin Donuts could start by no longer using those plastic cup covers that have a very short usage life but a very long trash life. Next, all fast food places could stop using any sort of plastic for drinks, utensils, plates, covers,and wrapping.
I think the cost of whatever alternative we come up with to match the convenience and public health features of plastic will be significantly outweighed by the reduced cost to our environment and reduced pollution.
What do you think?
Check out the great promotion by the Body Shop (image inset).
I'm going to be out at UMass Amherst visiting my PhD advisor, Craig Martin. He's been so kind to let me do a brown-bag discussion around DIYBio and Synth Bio:
Brown Bag Lunch Presentation and Discussion Do-It-Yourself Biology, Registry of Standardized Parts, iGEM, and more
ISB Conference Room 145
Wednesday, April 7, 2010
12:15pm
Alas, there was zippo name-recognition for DIYbio and Synth Bio (so much for all those news articles). So, Craig asked me to make a summary of some sort.
What it means to me: DIYBio is basically about increasing the tinkerability of
biology. While there are some who think there's science in DIYBio
("citizen science"), the current buzz is around making biology simpler
and more accessible outside of institutional settings - hacking,
basically. Folks are making $100 gel boxes, isolating bioluminescent
microbes from squid, building Dremel-based centrifuges, isolating DNA
from strawberries, or trying to figure out ways to make something
equivalent to Arduino for biology. It is a nascent "movement" drawing a
lot from the Open Source way of doing things and is still about hacking
and having fun and introducing people to the tools of biology. But, as in other areas, the expectation is that
interesting things will happen when tools became cheaper and more
approachable. How will that impact institutional science?
Synthetic Biology,
of the Biobricks flavor, seeks to create a standardized registry of
characterized biological parts to aid in the engineering of specified
micro-organisms. Much like standardized electronic parts paved the way
for the electronics industry, the expectation is that standardized
biological parts will lead to better engineering of micro-organism. Showcasing what can be done, there's an
annual jamboree for genetically engineered machines (iGEM) where
micro-organisms have been engineered to produce various pigments,
electrically stimulated light production, and detect explosives and
toxins. How will things change as it becomes easier to create defined
biological machines?
So what's the sales pitch? Why should anyone out at UMass care about these topics? DIYBio
and Synthetic Biology are re-arranging the way non-scientists engage
with biology. It's not really about science, but about making biology
more tinkerable, more hackable, more approachable so that the messiness
goes away and creativity can shine. Designers, engineers, and other non-biologists
are making biological tools and experimenting in fun and practical
ways. From melamine detectors to mine detectors, from bioluminescent
bacteria in squid isolated in the kitchen to electrically induced light
production in a lab, biology is starting to be more than just about
biology and more about machines. What does this mean to academic scientists? How might this change the future of biological science?
Enthusiastic? I guess I just want to get the word out. I feel that these two topics are changing the way folks view and use biology. And I think is some ways, making biology more accessible outside of the institutional setting will change what we can do with biology by opening access to whole new swaths of creative people.
Developing thought on biological tinkering and biological machines: Sure, biology-as-products exists today, in the form of breeding, brewing, bio-pharmaceuticals. But for me, in those cases the biology is serving the biology (as in, the protein is the drug, or the organism is the end-product). These engineered machines are using biological tools for non-biological purposes (such as toxin detectors or pixel generators)
I was having lunch with some old ex-lab friends. Unlike me, who left the lab at the end of the 90s, all three of them have kept on doing research and medicine and have their own labs with students, post-docs, and techs. The good news is that their research is progressing, the bad news is that funding is tighter than ever.
I had asked them who was writing a grant (of course, knowing that one always is writing some grant). There was an awkward pause as all three of them seemed to be lost in their thoughts, then they gave me an update of where things were at, since last I was in science, listing some stats to show how things were getting tighter.
When I left research, I had the naïve idea that I would no longer need to hustle for money. But, we all know, the biz world is just the same. Yet, for sure, the biz world seems to have a multitude of revenue and funding options that don't seem to be available to institutional scientists.
I feel that the whole endeavor of Science (I come from a biology background, so my thoughts are around that area, really) has been stuck in the 60s - the way we fund science, the expectations of the apprenticeship (PhD and Postdoc), the publishing and reputation cycle, the job progression - all seem to have been built in a model that came into being in the science boom of the 50s and 60s and really hasn't changed.
Am I missing something? I've been out 10 years, but it seems like nothing has improved. Funding is tighter, people still can't get academic jobs, and publishing is getting more onerous.
How do I envision the future of institutional science?
I'm not sure.
I've mentioned how science publishing could change, taking cues from the current way we use the Social Web. I think DIYBio points to how science could change how we explore the natural world and who does it. And, brilliant folks, like at Biocurious and Pink Army Coop, are looking at ways to diversify how we fund and participate in funding the future of science.
In summary, the business of institutional science is sclerotic and the clues to how we move forward are right in front of us. And, as usual, institutional culture is in the way of this change.
Do you think the way we do science should change? Can it? Will it in our lifetime? How do you envision the future of science or are we fine the way we are?
We had another gathering at The Sprouts. Mac, Jason, Jason, Dave, Kay, and I (with my son) gathered and talked about moving forward with safety stuff (pages, FAQs, and questionnaires), logo stuff, and playing around webcams.
We were going to do some wet-work, but the webcam seemed more interesting and we played with them, building a set up to see if we can use them like the folks at Hackteria.org did. In the process, we ended up taking microscopes apart so that we could have more fine control over the height of the slide.
Kinda funny to break up microscopes to build one.
Here are some pics of the afternoon (no video this time):
I was with my father this Thanksgiving and he asked me about "that Biology thing" I've been getting involved in. He's known for some time that I've been increasingly focused on science in the past few years and that, with my move back to the Boston area, I've been meeting up with scientists and biohackers.
I explained to him what Synthetic Biology and DIYbiology were all about. I showed him my video of my last DIYbio activity, who were the characters involved, what the impact has been so far.
Being a biz guy, he kept asking me what was the "end goal," to help him wrap his head around what would motivate folks to tinker with Biology. He wanted to know if there was a scientific goal or if there were products folks wanted to build.
After a long circular discussion, he finally realized that the field was so nascent that, really, the goal was to "increase the tinkerability" of Biology.
Of course, that conclusion is filtered through my view of where these areas are at. Right now, engineers and non-institutional biologists are mostly focused on simplifying and domesticating Biology. Issues like science and products will arise naturally as the accessibility and malleability of biological systems increases.
What do you think? Do you think that's an appropriate assessment?
Mac has written twoshort but deep posts, inspired by a talk by Sophia Roosth. What inspired Mac was Sophia's "anthropological insight" that DIYbio is "domesticating" Biology.
While I don't feel that it's an explicit doctrine, domestication of Biology is indeed the spirit of what DIYbiologists are up to. It's something that arises from the curiosity, openness, and tinkering that represents the DIYbiolgist "ethic." Sophia puts it in terms of "episteme" (Knowing) and "techne" (Doing).
Biology, as a discipline, is young in many ways - "science" itself is a product of the Enlightenment. And, as a focus of understanding, Biology is old - Aristotle was a biologist.
But domesticated Biology is at the core of civilization: thousands of years ago folks were breeding animals and plants, and brewing beer, bread, yogurt, and wine. These are the heart of Genetics and Microbiology and Biochemistry.
Mac made a recording of Sophia's talk. It's brilliant and really expresses DIYbio (and synthbio) as it is today and where it can lead. It's a must-listen for anyone interested in the future of Biology.
She makes a very nice story of the mind-sets of institutional and non-institutional scientists. And she pivots around the Homebrew Computer Club analogy as a way to think of the where DIYbio is going.
In many ways, she reminds me of the talks Dana Boyd gave, back in the day, as she watched the early evolution of social networking - Sophie brings together a range of threads from different disciplines to provide some coherence and understanding of the events and thinking unfolding right in front of us. Sophie has articulated what DIYbiologist just knew, just "did," in their hearts.
I think her insights just accelerate the nucleation of the "movement" at these early stages of exploration.
I've been meaning to share this for the longest time. I've had this book for ages and never tire of it.
"The Machinery of Life," by David Goodsell, is an illustrated journey through cells and proteins and macromolecules - at scale.
What I like about the book is that it attempts to show what it really looks like if you're the size of a molecule - the crowding, the relative sizes, and so on.
It's a really fascinating book for someone like me who has his head in the (molecular) clouds. :-)
There is a review of the original edition (PDF). A nice phrase from that review was "cellular numeracy," referring to the way Goodsell places things in scales, making us realize the relative sizes of molecules and cells.
At the iGEM Jamboree I saw a color image from Goodsell. After searching a bit, I now know that there is a color edition of the book (just out in 2009?), updated with new molecules, too. You can see more on Goodsell's own pages at Scripps.*
I highly recommend this book for anyone messing with molecules, to get a good idea of what the macromolecular landscape truly looks like.
Enjoy!
*It's a shame that the Scripps pages are so 1999-ish. The site needs to be more visual and more up to date.
I'm always interested in storytelling in its many guises, so the recent article titled "The internet is killing storytelling" was sure to catch my eye [I got it via @stephanierieger].
The author claims that in the modern hyper-connected society the long-form narrative, commonly seen in books, is losing out to the bite-sized snacking culture of the Web.
I read all the comments, many pointing out that narrative was alive and well, the Web full of all sorts of texts and stories and fan-fiction and such (long tail-ish and thru democratized creation and distribution). While a decent rebuttal of the author's thesis, these comments still missed one key fact (below).
Also, this article isn't really saying anything new, but bringing up a recurring theme. We've heard all this before, so it's a bit odd to see this thesis in a modern 2009 article. Indeed, I claim that this article is even weaker now than it would have been 5 years ago.
Why?
What all the commentors missed was that this whole article and all the comments focused solely on text as the medium for narrative. Humans have had many forms with which to tell stories - dance, art, song, theater, radio, TV - all of which are used in some form on the Web.
I claim that the Web has caused a huge transformation in non-text forms of narrative (in oral culture, as it were). We now have easy to use and widely available audio and visual tools and the Web has become a strong discovery and distribution mechanism for these productions. A scan of iTunes, Jamendo, YouTube, or Flickr will reveal of treasure trove of stories.
And, due to the temporary nature of digital media (either due to formatting issues or deletion or loss) we have more features of an oralculture than a literate culture. And that isn't bad. Unless one feels, like it seems this author does, that literary storytelling has primacy over other forms of storytelling.
Back in 2004 I was flying all over the place, promoting blogging. It was the year The Blogger entered the public eye, came out in magazines, built empires. One of the great debates was the clash between Main Stream Media (MSM) - the newspapers, publishing houses, and TV stations - versus the citizen journalist, the bedroom blogger, the unwashed masses of online writers.
MSM, of course, said that bloggers were not accurate, were not honest, were temporary, that only MSM was the font of Truth and quality information. Well, so much has happened since then. I feel there is still a place for professional journalism, but blogs have settled into their niches, providing a "long tail" (there I said it) of content of varying quality and scope. And, well, blogs today aren't the same as blogs 5 years ago, in the end, they are still just an online publication.
But watching the style and aspirations of the DIYbio crowd reminds me of those days. It seems that the friction between DIYbio types and Main Stream Scientists - the labs and institutes - hovers around the same issues as in the day of blogger vs. MSM.
And I think the change will be just as profound and the outcome just as mundane.
iGEM for me was the first time I got to meet folks in the DIYbio "movement." The DIYbio folks from NYC and Boston had a meeting the first night to discuss where things were going. They all knew each other and had collaborated in some areas.
It was nice to see the easy flow of ideas and decisions. As with iGEM, this group is in a very early stage. But already some things are becoming clear as to what it's going to take to keep growing.
One more thing (and I might be inviting a flame war): there is clearly some friction between the iGEM folks and the DIYbio folks. Part of this resides in prejudices towards amateur biologists (unfounded), part in worries about safety (well founded), part in the small difference in culture.
DIY home base One of the things that happened is that iGEM required teams to be affiliated with an institution. That was a way to ensure safety concerns (indeed, the FBI was a sponsor of the Jamboree, go figure). Independently, the DIYbio groups in Boston and NYC (and I) realized that, while it would be nice to actually do kitchen biology, groups need some sort of entity with which they can buy supplies, teach safety and techniques, and, of course, enter into iGEM.
I'm all for it. In the past months, reading and following and talking to DIYbio folks, my thoughts on hack-spaces has evolved to include more than just a bench, but also seminars, safety certification, mini-grants, and even a store (check out Pearl Biotech).
I was also glad to finally meet Mac, one of the leaders in DIYbio. He's recently purchased a lab trailer, full of equipment. He's now looking for space (too bad my ample backyard is so far from town). His goal is to build this out as a hack-space, also hoping to mix novice and experience biologists, to get some culture and skills transfer.
That's super. I look forward to getting more involved. Mac has a ton of projects in mind and could use some help. And I want to learn from the DIYbio NYC folks who recently formed a non-profit and are acquiring space so that they can get out of their living rooms and get a nice space to play around in.
This iGEM was my first. I'd read about it, talked about it, but this is the first time I've been immersed in it.
OK, so I wasn't part of a team, so I told folks I was a "lurker." That was out of the ordinary, since most folks were either staff, team members, or volunteers (which is what I should have done to save the registration fees - maybe).
Clever little undergrads I'm not going to go into details as to how the teams got to the Jamboree. Suffice it to say that anyone who wanted to come, came; also, the teams were undergraduates who thought long and hard on what they would build and then built everything over the summer.
I was impressed with the creativity the teams showed. There was light-induced vanillin production (for the aroma), electrically-induced light production (creating pixels - see video below), various detectors (for toxic metals and mines), and inducible pigment production (to free us of the boring tyranny of all the usual fluorescent reporter proteins).
While some might call for something applied to come out of all this, I am content to see the participant's enthusiasm; their learning of how to solve problems, think, and communicate results; the multi-disciplinary nature of teams, mixing engineers, biologist, sociologist, designers, mathematicians, physicists, artists, and programmers; and the gathering of like spirits to exchange information and dream up even more exciting things.
Keeping up with the E colis For me, it was heaven. I had not been immersed in this field in so long. It was good to try to figure things out, talk about how decisions were made, and learn all the clever techniques and solutions folks came up with.
Of course, at the end, I started dreaming up some of my own "machines." Who knows if I might be able to build one someday.
E. chromi I was particularly pleased with the winning team - Cambridge - for their creation of inducible pigmentation in bacteria. Through a network of connections, I had met the irrepressible Daisy Ginsberg, a designer from London who has been exploring the future world where synthetically engineered biological organisms are established and integrated into society. Daisy coined the term Kingdom Synthetica to add to the Eucarya-Bacteria-Archaea Kingdoms that we already have.
Daisy, and her partner in design-crime, James King, worked with the Cambridge team to help them explore the sociological and design aspects of what the team was building.* They got the team to think of a future that had colored bacteria and what that would mean. For example, one team talked about color-poachers killing rare wild-life for color genes; or, global battles over patenting of colors (for example, the Dutch if China were to patent Orange).
The best example of the future was colored poop, formed by these color producing bacteria detecting metabolic states and reporting it through color production, say green for an ulcer or red for vitamin deficiency (see picture). This colored poop was the sensation of the Jamboree. James and Daisy walked around with a silver valise, telling their whole story and ending with opening the valise, much to the surprise of their audience.
It was very fun.
Naming gaming Daisy christened the Cambridge bacteria as E chromi (@echromi on Twitter). And they presented their colored poop to the MOMA in NYC, so don't be surprised if the valise ends up there.
Once again, these names just point out that this Jamboree is more than a bunch of geeks building gadgets, but a whole way of thinking and mixing and creating. This is all so embryonic and what will come out of it no one really knows. But what is sure is that mixing folks from different background in a fertile playground with no dominant player is a sure way to come up with lots of interesting things.
Now I'll go off and start building my E coliroid (hm, what might that be?).
Here are some images and video that I took at iGEM:
*One nice feature of the competition was a thorough list of judging criteria, nudging the team to do more than just building something. Most interestingly, teams were encouraged to do a sociological survey around ethics, society, and synthbio. This added non-scientists to the teams. One of the most interesting findings (as these we mostly qualitative, due to experimental design constraints) was that folks were against genetically modified organisms (GMO) in general, but were fine with GMO use in humanitarian work, such as toxic waste or mine detection.
In this new era of natural philosophers (neo-natural philosophers?), where the cost of buying science kits and instruments can be an obstacle to amateur science, I keep thinking back to how science was done many years ago. What were the tools used? What were the different reagents of the day? How can this lost knowledge be applied today to circumvent barriers to modern reagent and instrument access?
I remember when I was a tech at MIT, back in the late 80s. There was an old Worthington molecular biology catalog with reagents and enzymes. For restriction enzymes, there were two: EcoRI and BamHI. Talking around the lab, our PI told me how "in the day" everyone had to purify their own restriction enzymes.
To me, that was fascinating. By the late 80s, the New England Biolabs catalog was already full of a ton of enzymes and kits. And, huh, it was so easy to sequence DNA by doing nested deletions of M13 vectors and using the kit's primers. And then you could purify plasmids with CsCl gradients and gobs of Ethidium Bromide in milligram balanced tubes and a wicked cool ultra-centrifuge.
State of the art, man!
As the junior tech in that lab at MIT, I was also responsible for keeping the fly stocks alive, transferring them on a regular basis from old bottles to new bottles. As per fruit fly science convention of the time, the flies were kept in small glass milk bottles, with cardboard plugs. I wonder how old our bottles were, but I was told that it was getting harder to find the bottles or even the cardboard plugs.
When I went over to the Whitehead to do some experiments, I saw that they all had plastic containers - in the shape of a milk bottle. It was the future, but in the image of the past. I wonder if folks today know why they still use such oddly shaped bottles to store flies in.
Straddling the past and future, that lab was a treasure trove of old stuff. I once opened a drawer at the lab and found a ton of capillary tubes with different color markings and sizes. These were actually glass micro-pipettes, calibrated and used with a mouth adapter (oh, my!), and eventually replaced by Gilsons with disposable plastic tips.
In summary, there are a ton of techniques and tools that have been knocked aside by kits and newer instruments, mostly for convenience (because I am a science history enthusiast, I have a ton of these stories). For those enterprising neo-natural philosophers, if you long for some kit or instrument, imagine back to the day when you got your hands dirty and didn't just buy your reagents. You might find some ideas how to create your own reagents and tools.
Image of pigments from hyperscholar, to remind you that "in the day" artists ground and mixed their own pigments to make paint. No kit for them!
I listen to NOVA's Science NOW podcasts. These are nice snippets of info, taken from NOVA's shows. Many of these snippets are also from Neil deGrasse Tyson, the head of the Museum of Natural History in NYC, and an amazing speaker.
The last episode I listened to was the Q&A session Tyson held at a monthly Science Pub, sponsored by the Oregon Museum of Science.
Event info: Portland Science Pub In this podcast, Neil deGrasse Tyson visits Portland, Oregon, to participate in a monthly event called the “Science Pub.” Sponsored by the Oregon Museum of Science and Industry, the “Pub” invites researchers to talk about their work, answer audience questions, and have a beer. It's a science conversation done Oregon style. The original event lasted over two hours, but we trimmed the Q&A down to about 30 minutes.
[link to mp3 of the event]
One of the questions raised was around the teachers that have made the most impact on you. Tyson showed that for most of us (expect for some strange dude who was an outlier) we have about five teachers who we remember best.
Of course, I'm thinking of my scientific career. And a few come readily to mind (these are folks who changed my thinking or I quote to this day). Now's a good time to thank some of them.
- Ms Strickland - My high school teacher. She not only introduced chemistry to me, but taught me many useful techniques that I used all throughout my science career. As my children start doing more serious science, I find myself teaching the things Ms Strickland taught me.
- Jim Garbe - Ok, not formally a teacher, but he was a grad student I worked closely with when I was a tech at MIT. He not only taught me a boatload of science and technique, but bathed me in the culture of science and being a scientist.
- Craig T Martin - My PhD advisor. He taught me TRUE molecular biology, feeding into my love of tinkering with molecules. He also taught me a lot on writing papers, and how to keep science fun. (He's recently been made head of the Chemistry Dept at UMass. Go, Craig!)
- Gary Silverman - My PI when I was a fellow. He taught me a lot about the business of academic research, such as running a lab, mentoring students, and grant writing.
I suppose I remember each of these as each provided support, information, and direction for each layer of being a scientist. From the basic introduction to the culture to the business, these folks were invested in making me a great scientist.
Thanks.
So, who are the teachers who you remember and contributed the most to who you are today?
Ben Hammersley, from Wired UK, wrote up an excellent article on synthetic biology with a bit of diybio mixed in (link below). Of course, the Knight and Shetty Biobricks were the center of the article, and provides a nice background to explain the concept behind standardized parts.
Link: At home with the DNA hackers:
Tom Knight, often called the "father" of biohacking, tells a joke: "A biologist goes into the lab one day, does an experiment and finds something is twice as complicated as she thought it was. 'Great,' she says, 'I get to write a paper.' An engineer goes into another lab, does an experiment, and she too finds something twice as complicated as she was expecting. 'Damn,' she says, 'Now how do I get rid of that?'"
The author of that article then touches upon DIYbio, and the trend to kitchen science. Knight, as usual, was concerned, but clear that he'd support it if DIYbiologists showed any competency. Interesting way to put it (and a good spin for things I am planning).
I was listening today to a podcast from Science Friday (highly recommended) on "The Age of Wonder," an interview of a science historian who spoke about the late 18th-, early 19th-century, when "science," as a descriptive term, did not exist. Back then, folks of all sorts of background, explored the world as "natural philosophers."
One story in particular, that Ira picked up on, was one such dabbler who discovered the anesthetic qualities of Nitrous Oxide but failed to put it in use, even with all the suffering from amputations during the Napoleonic Wars. Ira quickly asked if maybe because these guys were dabblers, they were exploring rather than looking for a solution or aware of the possibilities of applying what they discovered.
Might this be what Knight is thinking about DIYbiologists? While it's cool to think that folks can dabble with biology in their kitchen, does that prepare them for the safety issues, the problem solving, and potential serendipity as with an experienced biologist (or any craft)?
Chris Messina and Jyri Engeström wrote a brilliant article on the Arctic Startup site (hey, Ville and Antti, nice catch!). Both of them have been actively pushing forward the concept, philosophy, and hard-core standards for a more person-centric Web.
Link: The Web At A New Crossroads It’s 2009, going on 2010. For the past three years, the web has been morphing into a real-time and people-centric place. We’ve seen this trend among individual users — through their actions and demands for better social experiences — but also increasingly among companies and developers. We want a web that’s more “like us” than the old model was. We want a web where people are as important to the architecture of the system as documents.
They chart out the history of the Web and point to where it must go.
There have been some recent indicators, for example, an excellent article from Marshall Fitzpatrick (who is also brilliant and a watcher in this space), Opera's Unite, the anger at Facebook's purchase of Friendfeed, the rise of the Cloud, and the social meltdown the day Facebook and Twitter were down from DoS attacks (and some indicative comments of data ownership, and network ownership in some of my posts on Nokia Conversations). We seem to be passing a conceptual hurdle and behind-the-scenes coding (gosh, I had wished for DiSo back in 2008!) and finally seeing some real motion towards a more peer-to-peer style of social networking.
I was explaining to my son that in the old days, computing was done on main frames via terminals, much like social networking today is done from a dumb browser with servers in the Cloud. What Chris and Jyri are driving is just as liberating as PCs were to folks tied to mainframes - bringing power, choice, control, and the like back to the user, unmediated by proprietary services.
This isn't geeky dreaming. Chris, who had created Flock, which in some ways reflected a
person-centric form of browsing, has been able to pull together
Facebook, Myspace, Six Apart, and Google to back him up. And Jyri and Brad (who helped with the article) are key players in this and both work for Google (last I checked).
I admit I have not been following this as much as I used to. Other than the occasional article from Marshal that I pick up, in the past year or so, the most I have discussed this was at a lunch at Web 2.0 (where indeed, Chris, Jyri, and David Recordon, among others, were there going over all this stuff). So I am not sure what other articles these two have written.
In any case this article they have written will be part of the People-centric Real-time Web manifesto.
A colleague, John Markow, and I were discussing how to explain to people what features a piece of media should have to make it useful socially on the Web. We came up with this a long time ago and neither of us have written anything about this.
But I'm still regularly telling folks about this, so I though I could write it down once and for all.
Basically, we came up with five features a piece of media (the "object" below), say a photo or video, that will help it go out and socialize across the Web.
1) Search-able - If Google (or your site search engine) can't find it. It doesn't exist. 2) Link-able - the permalink 3) Comment-able - let folks comment on everything, build engagement 4) Embed-able - a key thing for me is that there is only one instance of the object, wich folks can them emed anywhere 5) Feed-able - some form of feed in which not only does this object show up, but that it's accessible right in the feed.
And that's it.
Bonus Karl Long, when I told him about this, added Remakable. Indeed, if the piece of media is krap, no amount of socializing features will help.
And an case-study In February, I received an email from a fellow colleague mentioning a video of a designer of the smallest Bluetooth headset Nokia had ever made, the Nokia Bluetooth Headset BH-804. The product page supposedly already contained the video.
I searched for the video on the Nokia.com site. No luck. I managed to find the product page but could not see the video. D'oh, it was hidden in a Flash button!
The image to the right shows where it is in case you go looking for it.
When I clicked on the button, I realized that for me to point to the video, I've have to give instructions, sine there was no direct link I could use.
Of course, since it was playing in a Flash player, and the video was stored on the Nokia.com servers, there was also no way for me to embed the video anywhere.And let's not even mention commenting or catching this video in a feed.
This video was basically stuck where it was put. Not social at all.
What we did was take this video, popped it into the Nokia Conversations YouTube channel. Being YouTube, the video was now search-able, link-able, comment-able, embed-able, and feed-able. We also promoted it with a post on the Nokia Conversations site, and put it into the right column video panel.
Ok, so, maybe the content wasn't so remarkable or interesting: To date, it has only received three thousand video views and two comments. And the article had two thousand views (half of which led to a video view) and one comment. But it was interesting enough that the three comments are quite enthusiastic and six sites thought it worthwhile to embed the video.
Not bad, eh?
And this story illustrates well the five (plus one) features for socializing media. Right?
I just found out that my thesis advisor is working on a cool project.
There's a new science building going up at UMass Amherst (where I got my PhD) and Craig T Martin (my thesis advisor) thought it would be cool to do an art installation where molecules are projected on the walls. He also realized that it would be cool if folks could interact with these molecules.
As he says on the project's site, molecules and chemicals are sort of "inaccessible and uninteresting" to the general public. His vision is to develop a large scale "molecular playground" where folks can actually go and manipulate the molecular projections.
Craig received a grant from the Camille & Henry Dreyfus Foundation to "develop and install in a prominent public space a
system for displaying large scale interactive molecules." The molecules will be animated and artistic, so that they can be appreciated even without direct manipulation.
Craig is collaborating with Allen Hanson from the UMass Amherst Computer Science Department.
Cool. I'm looking forward to seeing it.
And check out the video of a demo of the concept (below). The protein is HU, found in the bacterial nucleoid and involved in chromosome compaction. It makes a dramatic kink in DNA, and does some funky things. Check out the tongues going down the grooves on the opposite surface of the DNA. That's a tight grip. There more to it, though. You can manipulate the molecule yourself (with some explanations) on Craig's site.
There was a flurry of indignation recently on the DIYbio discussion group over an article in the Wall Street Journal over the safety of bio hackers (with added aggravation from Fox News' dramatic title to the exact same article).
Interestingly, this kind of alarm is not new, especially to biology. In the early days of molecular biology, there was a sudden panic that recombinant DNA was inherently unsafe. There was no basis to understand what was possible, what was ethically permissible, and what was unsafe.
Asilomar In a landmark event, that went on to change the nature of science policy and public outreach, Maxine Singer and Paul Berg, pioneers in molecular biology, assembled about 140 scientist, lawyers, and politicians to discuss the future of recombinant DNA.
The Asilomar Conference on Recombinant DNA, named after the place it was held at, addressed the principles for safely conducting recombinant DNA experiments, listing potential risks and outlining containment principles. The discussions also involved assessment of organisms, principles for choosing bacterial hosts, and what constituted good microbial practices. And finally, it explored the need for proper education and training of research personnel to carry out the recommendations that came out of the discussions.
There were a few interesting, non-science, aspects to this conference, as well. There was a desire to be transparent in the discussion and involve the public, to allay any fears non-scientists might have. Also, the Asilomar scientists drew up a series of voluntary guidelines rather than a regulatory body.
What can we learn? Asilomar is part of the culture and history of any molecular biologist (at least it was for me, I learned about it early in my career). Therefore, the precautionary thinking, the openness and public discourse, and the self-organizing regulation is part of molecular biology.
DIY biology is part of all this, and the same culture is part of a community that already is a cautious as it is curious and open. I am not sure if there's a need for an Asilomar for DIYbio, but with calls for licensing and calls from the FBI, clearly something definitive needs to be established.
It's been great to see the discussions around this by the DIYbio enthusiasts. They clearly understand the situation, now it's a matter of getting the message across.
In February, in a Barcelona restaurant, Mark Kramer caught up with me and asked me what I would be speaking about at the 3rd WLE Symposium (notes from the talk are in a preceding post).
He was kind enough to give me the video, so check it out below.
(and, no, I don't lisp like that - it's the audio quality)
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